With Sharepoint, when we want to upload a file, the “Add as a new version to existing file” is checked by default, and that could be an issue for you.

Here is a JavaScript fix to add into your masterpage, just before the </head> tag :
<script type="text/javascript">
function DefaultUploadOverwriteOff() {
if (document.title.indexOf("Upload Document") > -1) {
var input=document.querySelectorAll("input");
for (var i=input.length; i--;) {
if (input[i].id.search(/\_OverwriteSingle$|\_OverwriteMultiple$/) > -1) input[i].checked=false
}
}
}
_spBodyOnLoadFunctionNames.push('DefaultUploadOverwriteOff');
</script>
</head>